Hello Leigh,
If the employee has been marked as "Is Final", they will no longer be added or showing up in the pay event from a normal payrun as the system has considered that this is already the final payrun of the employee for the specific Financial Year.
For further assistance, we'd highly suggest you contacting our QuickBooks Online Support via Chat or Phone Support Hotline on this link: https://quickbooks.intuit.com/au/.
Best,
Anthony
